From 77b52a3fdfdb69a1fbd35d23aae5e05878de7018 Mon Sep 17 00:00:00 2001
From: Dasun Abeykoon <Dasun20202020@gmail.com>
Date: Fri, 27 Jun 2025 16:19:13 -0700
Subject: [PATCH 1/9] skpkg: migrate src folder

---
 .pre-commit-config.yaml             | 38 ++++++++++++++++++++---------
 src/diffpy/__init__.py              | 11 +--------
 src/diffpy/nmf_mapping/__init__.py  |  5 ++--
 src/diffpy/nmf_mapping/functions.py | 31 +++++++++++++++++++++++
 src/diffpy/nmf_mapping/version.py   |  5 ++--
 5 files changed, 62 insertions(+), 28 deletions(-)
 create mode 100644 src/diffpy/nmf_mapping/functions.py

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 9cf0556..0e4a84d 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,14 +1,14 @@
 default_language_version:
-    python: python3
+  python: python3
 ci:
-    autofix_commit_msg: |
-        [pre-commit.ci] auto fixes from pre-commit hooks
-    autofix_prs: true
-    autoupdate_branch: 'pre-commit-autoupdate'
-    autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
-    autoupdate_schedule: monthly
-    skip: [no-commit-to-branch]
-    submodules: false
+  autofix_commit_msg: |
+    [pre-commit.ci] auto fixes from pre-commit hooks
+  autofix_prs: true
+  autoupdate_branch: "pre-commit-autoupdate"
+  autoupdate_commit_msg: "[pre-commit.ci] pre-commit autoupdate"
+  autoupdate_schedule: monthly
+  skip: [no-commit-to-branch]
+  submodules: false
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.6.0
@@ -47,6 +47,20 @@ repos:
   - repo: https://github.com/codespell-project/codespell
     rev: v2.3.0
     hooks:
-    - id: codespell
-      additional_dependencies:
-        - tomli
+      - id: codespell
+        additional_dependencies:
+          - tomli
+  # prettier - multi formatter for .json, .yml, and .md files
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: f12edd9c7be1c20cfa42420fd0e6df71e42b51ea # frozen: v4.0.0-alpha.8
+    hooks:
+      - id: prettier
+        additional_dependencies:
+          - "prettier@^3.2.4"
+  # docformatter - PEP 257 compliant docstring formatter
+  - repo: https://github.com/s-weigand/docformatter
+    rev: 5757c5190d95e5449f102ace83df92e7d3b06c6c
+    hooks:
+      - id: docformatter
+        additional_dependencies: [tomli]
+        args: [--in-place, --config, ./pyproject.toml]
diff --git a/src/diffpy/__init__.py b/src/diffpy/__init__.py
index 58c58be..1584c1d 100644
--- a/src/diffpy/__init__.py
+++ b/src/diffpy/__init__.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# (c) 2024 The Trustees of Columbia University in the City of New York.
+# (c) 2025 The Trustees of Columbia University in the City of New York.
 # All rights reserved.
 #
 # File coded by: Billinge Group members and community contributors.
@@ -12,12 +12,3 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-
-"""Blank namespace package for module diffpy."""
-
-
-from pkgutil import extend_path
-
-__path__ = extend_path(__path__, __name__)
-
-# End of file
diff --git a/src/diffpy/nmf_mapping/__init__.py b/src/diffpy/nmf_mapping/__init__.py
index 031f6ef..6e3c01f 100644
--- a/src/diffpy/nmf_mapping/__init__.py
+++ b/src/diffpy/nmf_mapping/__init__.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# (c) 2024 The Trustees of Columbia University in the City of New York.
+# (c) 2025 The Trustees of Columbia University in the City of New York.
 # All rights reserved.
 #
 # File coded by: Billinge Group members and community contributors.
@@ -12,11 +12,10 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-
 """Python package for running NMF analysis on PDF and XRD data."""
 
 # package version
-from diffpy.nmf_mapping.version import __version__
+from diffpy.nmf_mapping.version import __version__  # noqa
 
 # silence the pyflakes syntax checker
 assert __version__ or True
diff --git a/src/diffpy/nmf_mapping/functions.py b/src/diffpy/nmf_mapping/functions.py
new file mode 100644
index 0000000..e7e2c8e
--- /dev/null
+++ b/src/diffpy/nmf_mapping/functions.py
@@ -0,0 +1,31 @@
+import numpy as np
+
+
+def dot_product(a, b):
+    """Compute the dot product of two vectors of any size.
+
+    Ensure that the inputs, a and b, are of the same size.
+    The supported types are "array_like" objects, which can
+    be converted to a NumPy array. Examples include lists and tuples.
+
+    Parameters
+    ----------
+    a : array_like
+        The first input vector.
+    b : array_like
+        The second input vector.
+
+    Returns
+    -------
+    float
+        The dot product of the two vectors.
+
+    Examples
+    --------
+    Compute the dot product of two lists:
+    >>> a = [1, 2, 3]
+    >>> b = [4, 5, 6]
+    >>> dot_product(a, b)
+    32.0
+    """
+    return float(np.dot(a, b))
diff --git a/src/diffpy/nmf_mapping/version.py b/src/diffpy/nmf_mapping/version.py
index 0991a0b..dc2d4e4 100644
--- a/src/diffpy/nmf_mapping/version.py
+++ b/src/diffpy/nmf_mapping/version.py
@@ -1,18 +1,17 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# (c) 2024 The Trustees of Columbia University in the City of New York.
+# (c) 2025 The Trustees of Columbia University in the City of New York.
 # All rights reserved.
 #
 # File coded by: Billinge Group members and community contributors.
 #
 # See GitHub contributions for a more detailed list of contributors.
-# https://github.com/diffpy/diffpy.nmf_mapping/graphs/contributors
+# https://github.com/diffpy/diffpy.nmf_mapping/graphs/contributors  # noqa: E501
 #
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-
 """Definition of __version__."""
 
 #  We do not use the other three variables, but can be added back if needed.

From 6eba0054e5ec2639a7d0f8c540b3dbea4295bc68 Mon Sep 17 00:00:00 2001
From: Dasun Abeykoon <Dasun20202020@gmail.com>
Date: Fri, 27 Jun 2025 16:20:32 -0700
Subject: [PATCH 2/9] skpkg: add tests folder

---
 tests/test_functions.py | 40 ++++++++++++++++++++++++++++++++++++++++
 tests/test_version.py   |  8 ++++----
 2 files changed, 44 insertions(+), 4 deletions(-)
 create mode 100644 tests/test_functions.py

diff --git a/tests/test_functions.py b/tests/test_functions.py
new file mode 100644
index 0000000..77a5233
--- /dev/null
+++ b/tests/test_functions.py
@@ -0,0 +1,40 @@
+import numpy as np
+import pytest
+
+from diffpy.nmf_mapping import functions  # noqa
+
+
+def test_dot_product_2D_list():
+    a = [1, 2]
+    b = [3, 4]
+    expected = 11.0
+    actual = functions.dot_product(a, b)
+    assert actual == expected
+
+
+def test_dot_product_3D_list():
+    a = [1, 2, 3]
+    b = [4, 5, 6]
+    expected = 32.0
+    actual = functions.dot_product(a, b)
+    assert actual == expected
+
+
+@pytest.mark.parametrize(
+    "a, b, expected",
+    [
+        # Test whether the dot product function works with 2D and 3D vectors
+        # C1: lists, expect correct float output
+        ([1, 2], [3, 4], 11.0),
+        ([1, 2, 3], [4, 5, 6], 32.0),
+        # C2: tuples, expect correct float output
+        ((1, 2), (3, 4), 11.0),
+        ((1, 2, 3), (4, 5, 6), 32.0),
+        # C3: numpy arrays, expect correct float output
+        (np.array([1, 2]), np.array([3, 4]), 11.0),
+        (np.array([1, 2, 3]), np.array([4, 5, 6]), 32.0),
+    ],
+)
+def test_dot_product(a, b, expected):
+    actual = functions.dot_product(a, b)
+    assert actual == expected
diff --git a/tests/test_version.py b/tests/test_version.py
index 1167910..f9d0038 100644
--- a/tests/test_version.py
+++ b/tests/test_version.py
@@ -1,10 +1,10 @@
-"""Unit tests for __version__.py
-"""
+"""Unit tests for __version__.py."""
 
-import diffpy.nmf_mapping
+import diffpy.nmf_mapping  # noqa
 
 
 def test_package_version():
-    """Ensure the package version is defined and not set to the initial placeholder."""
+    """Ensure the package version is defined and not set to the initial
+    placeholder."""
     assert hasattr(diffpy.nmf_mapping, "__version__")
     assert diffpy.nmf_mapping.__version__ != "0.0.0"

From b997d01b5584d878c8deb4fc3009a76f56d22ceb Mon Sep 17 00:00:00 2001
From: Dasun Abeykoon <Dasun20202020@gmail.com>
Date: Fri, 27 Jun 2025 16:23:23 -0700
Subject: [PATCH 3/9] skpkg: list dependencies in requirement folder

---
 requirements/build.txt | 0
 requirements/docs.txt  | 1 +
 2 files changed, 1 insertion(+)
 delete mode 100644 requirements/build.txt

diff --git a/requirements/build.txt b/requirements/build.txt
deleted file mode 100644
index e69de29..0000000
diff --git a/requirements/docs.txt b/requirements/docs.txt
index ab17b1c..5f34c6e 100644
--- a/requirements/docs.txt
+++ b/requirements/docs.txt
@@ -1,4 +1,5 @@
 sphinx
 sphinx_rtd_theme
+sphinx-copybutton
 doctr
 m2r

From 4f451aa5dfec714602cbb8c9d6786f4df28d61bb Mon Sep 17 00:00:00 2001
From: Dasun Abeykoon <Dasun20202020@gmail.com>
Date: Fri, 27 Jun 2025 16:35:23 -0700
Subject: [PATCH 4/9] skpkg: add CI and issue/PR templates

---
 .github/workflows/tests-on-pr.yml | 9 +++------
 .gitignore                        | 8 +-------
 2 files changed, 4 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/tests-on-pr.yml b/.github/workflows/tests-on-pr.yml
index 766a79d..3245cde 100644
--- a/.github/workflows/tests-on-pr.yml
+++ b/.github/workflows/tests-on-pr.yml
@@ -1,18 +1,15 @@
 name: Tests on PR
 
 on:
-  push:
-    branches:
-      - main
   pull_request:
   workflow_dispatch:
 
 jobs:
-  validate:
-    uses: Billingegroup/release-scripts/.github/workflows/_tests-on-pr.yml@v0
+  tests-on-pr:
+    uses: scikit-package/release-scripts/.github/workflows/_tests-on-pr.yml@v0
     with:
       project: diffpy.nmf_mapping
       c_extension: false
-      headless: false
+      headless: true
     secrets:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
diff --git a/.gitignore b/.gitignore
index a25212e..099e294 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,6 +10,7 @@ __pycache__/
 .Python
 env/
 build/
+_build/
 develop-eggs/
 dist/
 downloads/
@@ -90,10 +91,3 @@ target/
 
 # Ipython Notebook
 .ipynb_checkpoints
-
-# version information
-setup.cfg
-/src/diffpy/*/version.cfg
-
-# Rever
-rever/

From f73b3eaf603ccd7c53b6fb07bdb5f0ce0e4f6874 Mon Sep 17 00:00:00 2001
From: Dasun Abeykoon <Dasun20202020@gmail.com>
Date: Fri, 27 Jun 2025 16:36:41 -0700
Subject: [PATCH 5/9] skpkg: add pyproject.toml

---
 pyproject.toml | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index c906f67..6094416 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,13 +6,13 @@ build-backend = "setuptools.build_meta"
 name = "diffpy.nmf_mapping"
 dynamic=['version', 'dependencies']
 authors = [
-  { name="Simon J.L. Billinge group", email="simon.billinge@gmail.com" },
+  { name="Simon J.L. Billinge group", email="sb2896@columbia.edu" },
 ]
 maintainers = [
-  { name="Simon J.L. Billinge group", email="simon.billinge@gmail.com" },
+  { name="Simon J.L. Billinge group", email="sb2896@columbia.edu" },
 ]
 description = "Python package for running NMF analysis on PDF and XRD data."
-keywords = ['"diffpy"', '"PDF"', '"NMF"']
+keywords = ['diffpy', 'PDF', 'NMF']
 readme = "README.rst"
 requires-python = ">=3.11, <3.14"
 classifiers = [
@@ -42,9 +42,6 @@ template = "{tag}"
 dev_template = "{tag}"
 dirty_template = "{tag}"
 
-[project.scripts]
-snmf = "diffpy.nmf_mapping.main:main"
-
 [tool.setuptools.packages.find]
 where = ["src"]  # list of folders that contain the packages (["."] by default)
 include = ["*"]  # package names should match these glob patterns (["*"] by default)
@@ -59,8 +56,13 @@ exclude-file = ".codespell/ignore_lines.txt"
 ignore-words = ".codespell/ignore_words.txt"
 skip = "*.cif,*.dat"
 
+[tool.docformatter]
+recursive = true
+wrap-summaries = 72
+wrap-descriptions = 72
+
 [tool.black]
-line-length = 115
+line-length = 79
 include = '\.pyi?$'
 exclude = '''
 /(

From 1f6f59d5165eddce5aa9d21e147823530cfb18c9 Mon Sep 17 00:00:00 2001
From: Dasun Abeykoon <Dasun20202020@gmail.com>
Date: Fri, 27 Jun 2025 16:41:23 -0700
Subject: [PATCH 6/9] chore: revert uneeded deletion

---
 pyproject.toml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 6094416..d50abc8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -42,6 +42,9 @@ template = "{tag}"
 dev_template = "{tag}"
 dirty_template = "{tag}"
 
+[project.scripts]
+snmf = "diffpy.nmf_mapping.main:main"
+
 [tool.setuptools.packages.find]
 where = ["src"]  # list of folders that contain the packages (["."] by default)
 include = ["*"]  # package names should match these glob patterns (["*"] by default)
@@ -62,7 +65,7 @@ wrap-summaries = 72
 wrap-descriptions = 72
 
 [tool.black]
-line-length = 79
+line-length = 115
 include = '\.pyi?$'
 exclude = '''
 /(

From 201d0ea92fcfb967448bbf3c2e8c7bc0b85b6f16 Mon Sep 17 00:00:00 2001
From: Dasun Abeykoon <Dasun20202020@gmail.com>
Date: Fri, 27 Jun 2025 16:47:25 -0700
Subject: [PATCH 7/9] chore: reverted uneeded changes in src directory

---
 src/diffpy/__init__.py              | 11 +++++++++-
 src/diffpy/nmf_mapping/__init__.py  |  2 +-
 src/diffpy/nmf_mapping/functions.py | 31 -----------------------------
 src/diffpy/nmf_mapping/version.py   |  2 +-
 4 files changed, 12 insertions(+), 34 deletions(-)
 delete mode 100644 src/diffpy/nmf_mapping/functions.py

diff --git a/src/diffpy/__init__.py b/src/diffpy/__init__.py
index 1584c1d..256c067 100644
--- a/src/diffpy/__init__.py
+++ b/src/diffpy/__init__.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# (c) 2025 The Trustees of Columbia University in the City of New York.
+# (c) 2024-2025 The Trustees of Columbia University in the City of New York.
 # All rights reserved.
 #
 # File coded by: Billinge Group members and community contributors.
@@ -12,3 +12,12 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
+
+"""Blank namespace package for module diffpy."""
+
+
+from pkgutil import extend_path
+
+__path__ = extend_path(__path__, __name__)
+
+# End of file
diff --git a/src/diffpy/nmf_mapping/__init__.py b/src/diffpy/nmf_mapping/__init__.py
index 6e3c01f..c6eb4f6 100644
--- a/src/diffpy/nmf_mapping/__init__.py
+++ b/src/diffpy/nmf_mapping/__init__.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# (c) 2025 The Trustees of Columbia University in the City of New York.
+# (c) 2024-2025 The Trustees of Columbia University in the City of New York.
 # All rights reserved.
 #
 # File coded by: Billinge Group members and community contributors.
diff --git a/src/diffpy/nmf_mapping/functions.py b/src/diffpy/nmf_mapping/functions.py
deleted file mode 100644
index e7e2c8e..0000000
--- a/src/diffpy/nmf_mapping/functions.py
+++ /dev/null
@@ -1,31 +0,0 @@
-import numpy as np
-
-
-def dot_product(a, b):
-    """Compute the dot product of two vectors of any size.
-
-    Ensure that the inputs, a and b, are of the same size.
-    The supported types are "array_like" objects, which can
-    be converted to a NumPy array. Examples include lists and tuples.
-
-    Parameters
-    ----------
-    a : array_like
-        The first input vector.
-    b : array_like
-        The second input vector.
-
-    Returns
-    -------
-    float
-        The dot product of the two vectors.
-
-    Examples
-    --------
-    Compute the dot product of two lists:
-    >>> a = [1, 2, 3]
-    >>> b = [4, 5, 6]
-    >>> dot_product(a, b)
-    32.0
-    """
-    return float(np.dot(a, b))
diff --git a/src/diffpy/nmf_mapping/version.py b/src/diffpy/nmf_mapping/version.py
index dc2d4e4..fd17c35 100644
--- a/src/diffpy/nmf_mapping/version.py
+++ b/src/diffpy/nmf_mapping/version.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# (c) 2025 The Trustees of Columbia University in the City of New York.
+# (c) 2024-2025 The Trustees of Columbia University in the City of New York.
 # All rights reserved.
 #
 # File coded by: Billinge Group members and community contributors.

From 914fbc305f5962c3c4886e50dd5a39a88baf8b5b Mon Sep 17 00:00:00 2001
From: Dasun Abeykoon <Dasun20202020@gmail.com>
Date: Fri, 27 Jun 2025 16:47:54 -0700
Subject: [PATCH 8/9] chore: reverted uneeded changes in tests directory

---
 tests/test_functions.py | 40 ----------------------------------------
 1 file changed, 40 deletions(-)
 delete mode 100644 tests/test_functions.py

diff --git a/tests/test_functions.py b/tests/test_functions.py
deleted file mode 100644
index 77a5233..0000000
--- a/tests/test_functions.py
+++ /dev/null
@@ -1,40 +0,0 @@
-import numpy as np
-import pytest
-
-from diffpy.nmf_mapping import functions  # noqa
-
-
-def test_dot_product_2D_list():
-    a = [1, 2]
-    b = [3, 4]
-    expected = 11.0
-    actual = functions.dot_product(a, b)
-    assert actual == expected
-
-
-def test_dot_product_3D_list():
-    a = [1, 2, 3]
-    b = [4, 5, 6]
-    expected = 32.0
-    actual = functions.dot_product(a, b)
-    assert actual == expected
-
-
-@pytest.mark.parametrize(
-    "a, b, expected",
-    [
-        # Test whether the dot product function works with 2D and 3D vectors
-        # C1: lists, expect correct float output
-        ([1, 2], [3, 4], 11.0),
-        ([1, 2, 3], [4, 5, 6], 32.0),
-        # C2: tuples, expect correct float output
-        ((1, 2), (3, 4), 11.0),
-        ((1, 2, 3), (4, 5, 6), 32.0),
-        # C3: numpy arrays, expect correct float output
-        (np.array([1, 2]), np.array([3, 4]), 11.0),
-        (np.array([1, 2, 3]), np.array([4, 5, 6]), 32.0),
-    ],
-)
-def test_dot_product(a, b, expected):
-    actual = functions.dot_product(a, b)
-    assert actual == expected

From 345116dd080d2040eafa1b76ed3ba90eb74d0a39 Mon Sep 17 00:00:00 2001
From: Dasun Abeykoon <Dasun20202020@gmail.com>
Date: Sat, 28 Jun 2025 09:40:42 -0700
Subject: [PATCH 9/9] Fix: set headless to false for test-on-PR gh workflow

Signed-off-by: Dasun Abeykoon <Dasun20202020@gmail.com>
---
 .github/workflows/tests-on-pr.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests-on-pr.yml b/.github/workflows/tests-on-pr.yml
index 3245cde..6de41f3 100644
--- a/.github/workflows/tests-on-pr.yml
+++ b/.github/workflows/tests-on-pr.yml
@@ -10,6 +10,6 @@ jobs:
     with:
       project: diffpy.nmf_mapping
       c_extension: false
-      headless: true
+      headless: false
     secrets:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}